zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Better support for specifying read filters to apply directly from the walkers. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1212 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-07-09 23:59:53 +00:00
parent ce08f5f0c3
commit 03e1713988
13 changed files with 263 additions and 132 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

36
java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
View File

@ -50,13 +50,8 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
/** the type of analysis to run - switch to the type of analysis */
private String analysisName = "SomaticCoverageWalker";
// our walker manager
private WalkerManager walkerManager = null;
// our genome analysis engine
private GenomeAnalysisEngine GATKEngine = null;
public String pluginPathName = null;
private GenomeAnalysisEngine GATKEngine = new GenomeAnalysisEngine();
// get the analysis name
protected abstract String getAnalysisName();
@ -71,17 +66,7 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
* @return the return code to exit the program with
*/
protected int execute() {
// create the walker
Walker<?, ?> mWalker = null;
try {
mWalker = walkerManager.createWalkerByName(analysisName);
} catch (InstantiationException ex) {
throw new RuntimeException("Unable to instantiate walker.", ex);
}
catch (IllegalAccessException ex) {
throw new RuntimeException("Unable to access walker", ex);
}
Walker<?,?> mWalker = GATKEngine.getWalkerByName(analysisName);
// load the arguments into the walkers
loadArgumentsIntoObject(argCollection);
@ -93,7 +78,7 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
// set the analysis name in the argument collection
this.argCollection.analysisName = this.analysisName;
try {
GATKEngine = new GenomeAnalysisEngine(argCollection, mWalker);
GATKEngine.execute(argCollection, mWalker);
}
catch (ArgumentException ex) {
// Rethrow argument exceptions. Let the command-line argument do what it's designed to do.
@ -124,20 +109,9 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
*/
@Override
protected Class[] getArgumentSources() {
// get the analysis name from the overriding class
analysisName = this.getAnalysisName();
// get any argument overrides they want to present
overrideArguments();
// No walker info? No plugins.
if (analysisName == null) return new Class[]{};
walkerManager = new WalkerManager(pluginPathName);
if (!walkerManager.doesWalkerExist(analysisName))
throw new IllegalArgumentException("Invalid analysis name");
return new Class[]{walkerManager.getWalkerClassByName(analysisName)};
if (analysisName == null) return new Class[] {};
return new Class[] { GATKEngine.getWalkerByName(analysisName).getClass() };
}

35
java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
View File

@ -1,7 +1,6 @@
package org.broadinstitute.sting.gatk;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.xReadLines;
import org.broadinstitute.sting.utils.cmdLine.*;
@ -49,14 +48,8 @@ public class CommandLineGATK extends CommandLineProgram {
@ArgumentCollection // our argument collection, the collection of command line args we accept
public GATKArgumentCollection argCollection = new GATKArgumentCollection();
public String pluginPathName = null;
// our genome analysis engine
GenomeAnalysisEngine GATKEngine = null;
// our walker manager
private WalkerManager walkerManager = null;
/** our genome analysis engine */
GenomeAnalysisEngine GATKEngine = new GenomeAnalysisEngine();
/** Required main method implementation. */
public static void main(String[] argv) {
@ -68,7 +61,6 @@ public class CommandLineGATK extends CommandLineProgram {
}
}
/**
* this is the function that the inheriting class can expect to have called
* when the command line system has initialized.
@ -76,15 +68,8 @@ public class CommandLineGATK extends CommandLineProgram {
* @return the return code to exit the program with
*/
protected int execute() {
Walker<?, ?> mWalker = null;
try {
mWalker = walkerManager.createWalkerByName(analysisName);
} catch (InstantiationException ex) {
throw new RuntimeException("Unable to instantiate walker.", ex);
}
catch (IllegalAccessException ex) {
throw new RuntimeException("Unable to access walker", ex);
}
Walker<?,?> mWalker = GATKEngine.getWalkerByName(analysisName);
loadArgumentsIntoObject(argCollection);
loadArgumentsIntoObject(mWalker);
@ -92,11 +77,11 @@ public class CommandLineGATK extends CommandLineProgram {
this.argCollection.analysisName = this.analysisName;
try {
GATKEngine = new GenomeAnalysisEngine(argCollection, mWalker);
GATKEngine.execute(argCollection, mWalker);
}
catch (ArgumentException ex) {
// Rethrow argument exceptions. Let the command-line argument do what it's designed to do.
throw ex;
throw ex;
}
catch (StingException exp) {
System.err.println("Caught StingException. It's message is " + exp.getMessage());
@ -125,13 +110,7 @@ public class CommandLineGATK extends CommandLineProgram {
protected Class[] getArgumentSources() {
// No walker info? No plugins.
if (analysisName == null) return new Class[] {};
walkerManager = new WalkerManager(pluginPathName);
if (!walkerManager.doesWalkerExist(analysisName))
throw new IllegalArgumentException("Invalid analysis name");
return new Class[]{walkerManager.getWalkerClassByName(analysisName)};
return new Class[] { GATKEngine.getWalkerByName(analysisName).getClass() };
}
@Override

91
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
View File

@ -27,12 +27,14 @@ package org.broadinstitute.sting.gatk;
import net.sf.picard.reference.ReferenceSequenceFile;
import net.sf.picard.reference.ReferenceSequenceFileFactory;
import net.sf.picard.filter.SamRecordFilter;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.executive.MicroScheduler;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.cmdLine.ArgumentException;
@ -50,7 +52,7 @@ public class GenomeAnalysisEngine {
private TraversalEngine engine = null;
// our argument collection
private final GATKArgumentCollection argCollection;
private GATKArgumentCollection argCollection;
/** Collection of output streams used by the walker. */
private OutputTracker outputTracker = null;
@ -58,8 +60,11 @@ public class GenomeAnalysisEngine {
/** our log, which we want to capture anything from this class */
private static Logger logger = Logger.getLogger(GenomeAnalysisEngine.class);
/** the return value from our walker */
private Object walkerReturn = null;
/** our walker manager */
private final WalkerManager walkerManager;
/** plugin path for the walker manager. */
public final String pluginPathName = null;
/**
* our constructor, where all the work is done
@ -67,22 +72,31 @@ public class GenomeAnalysisEngine {
* legacy traversal types are sent to legacyTraversal function; as we move more of the traversals to the
* new MicroScheduler class we'll be able to delete that function.
*
* @param args the argument collection, where we get all our setup information from
* @param my_walker the walker we're running with
*/
public GenomeAnalysisEngine(GATKArgumentCollection args, Walker my_walker) {
public GenomeAnalysisEngine() {
// make sure our instance variable points to this analysis engine
instance = this;
walkerManager = new WalkerManager(pluginPathName);
}
/**
* Actually run the GATK with the specified walker.
* @param args the argument collection, where we get all our setup information from
* @param my_walker Walker to run over the dataset. Must not be null.
*/
public Object execute(GATKArgumentCollection args, Walker<?,?> my_walker) {
// validate our parameters
if (args == null) {
throw new StingException("The GATKArgumentCollection passed to GenomeAnalysisEngine can be null.");
}
// validate our parameters
if (args == null || my_walker == null) {
throw new StingException("Neither the GATKArgumentCollection or the Walker passed to GenomeAnalysisEngine can be null.");
}
if (my_walker == null)
throw new StingException("The walker passed to GenomeAnalysisEngine can be null.");
// save our argument parameter
this.argCollection = args;
// make sure our instance variable points to this analysis engine
instance = this;
// our reference ordered data collection
List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods = new ArrayList<ReferenceOrderedData<? extends ReferenceOrderedDatum>>();
@ -129,9 +143,26 @@ public class GenomeAnalysisEngine {
locs = GenomeLocSortedSet.createSetFromList(parseIntervalRegion(argCollection.intervals));
}
// excute the microscheduler, storing the results
walkerReturn = microScheduler.execute(my_walker, locs, argCollection.maximumEngineIterations);
return microScheduler.execute(my_walker, locs, argCollection.maximumEngineIterations);
}
/**
* Retrieves an instance of the walker based on the walker name.
* @param walkerName Name of the walker. Must not be null. If the walker cannot be instantiated, an exception will be thrown.
* @return An instance of the walker.
*/
public Walker<?,?> getWalkerByName( String walkerName ) {
try {
return walkerManager.createWalkerByName(walkerName);
} catch (InstantiationException ex) {
throw new StingException("Unable to instantiate walker.", ex);
}
catch (IllegalAccessException ex) {
throw new StingException("Unable to access walker", ex);
}
}
/**
* setup a microscheduler
*
@ -147,12 +178,12 @@ public class GenomeAnalysisEngine {
// we need to verify different parameter based on the walker type
if (my_walker instanceof LocusWalker || my_walker instanceof LocusWindowWalker) {
// create the MicroScheduler
microScheduler = MicroScheduler.create(my_walker, extractSourceInfoFromArguments(argCollection), argCollection.referenceFile, rods, argCollection.numberOfThreads);
microScheduler = MicroScheduler.create(my_walker, extractSourceInfo(my_walker,argCollection), argCollection.referenceFile, rods, argCollection.numberOfThreads);
engine = microScheduler.getTraversalEngine();
} else if (my_walker instanceof ReadWalker || my_walker instanceof DuplicateWalker) {
if (argCollection.referenceFile == null)
Utils.scareUser(String.format("Read-based traversals require a reference file but none was given"));
microScheduler = MicroScheduler.create(my_walker, extractSourceInfoFromArguments(argCollection), argCollection.referenceFile, rods, argCollection.numberOfThreads);
microScheduler = MicroScheduler.create(my_walker, extractSourceInfo(my_walker,argCollection), argCollection.referenceFile, rods, argCollection.numberOfThreads);
engine = microScheduler.getTraversalEngine();
} else {
Utils.scareUser(String.format("Unable to create the appropriate TraversalEngine for analysis type " + argCollection.analysisName));
@ -191,18 +222,24 @@ public class GenomeAnalysisEngine {
/**
* Bundles all the source information about the reads into a unified data structure.
*
* @param walker The walker for which to extract info.
* @param argCollection The collection of arguments passed to the engine.
*
* @return The reads object providing reads source info.
*/
private Reads extractSourceInfo( Walker walker, GATKArgumentCollection argCollection ) {
List<SamRecordFilter> filters = new ArrayList<SamRecordFilter>();
private Reads extractSourceInfoFromArguments(GATKArgumentCollection argCollection) {
return new Reads(argCollection.samFiles,
argCollection.strictnessLevel,
argCollection.downsampleFraction,
argCollection.downsampleCoverage,
!argCollection.unsafe,
argCollection.filterZeroMappingQualityReads);
filters.addAll( WalkerManager.getReadFilters(walker) );
if( argCollection.filterZeroMappingQualityReads != null && argCollection.filterZeroMappingQualityReads )
filters.add( new ZeroMappingQualityReadFilter() );
return new Reads( argCollection.samFiles,
argCollection.strictnessLevel,
argCollection.downsampleFraction,
argCollection.downsampleCoverage,
!argCollection.unsafe,
filters );
}
private void validateInputsAgainstWalker(Walker walker,
@ -297,14 +334,4 @@ public class GenomeAnalysisEngine {
public GATKArgumentCollection getArguments() {
return this.argCollection;
}
/**
* Get's the return value of the walker
*
* @return an Object representing the return value of the walker
*/
public Object getWalkerReturn() {
return walkerReturn;
}
}

19
java/src/org/broadinstitute/sting/gatk/Reads.java
View File

@ -1,13 +1,11 @@
package org.broadinstitute.sting.gatk;
import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
import org.broadinstitute.sting.utils.StingException;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.List;
import java.util.ArrayList;
import net.sf.samtools.SAMFileReader;
import net.sf.picard.filter.SamRecordFilter;
/**
* User: hanna
* Date: May 14, 2009
@ -31,7 +29,7 @@ public class Reads {
private Double downsamplingFraction = null;
private Integer downsampleToCoverage = null;
private Boolean beSafe = null;
private Boolean filterZeroMappingQualityReads = null;
private List<SamRecordFilter> supplementalFilters = null;
/**
* Gets a list of the files acting as sources of reads.
@ -73,8 +71,8 @@ public class Reads {
return beSafe;
}
public Boolean getFilterZeroMappingQualityReads() {
return filterZeroMappingQualityReads;
public List<SamRecordFilter> getSupplementalFilters() {
return supplementalFilters;
}
/**
@ -83,6 +81,7 @@ public class Reads {
*/
public Reads( List<File> readsFiles ) {
this.readsFiles = readsFiles;
this.supplementalFilters = new ArrayList<SamRecordFilter>();
}
/**
@ -94,19 +93,19 @@ public class Reads {
* @param downsampleFraction fraction of reads to downsample.
* @param downsampleCoverage downsampling per-locus.
* @param beSafe Whether to enable safety checking.
* @param filterZeroMappingQualityReads whether to filter zero mapping quality reads.
* @param supplementalFilters additional filters to dynamically apply.
*/
Reads( List<File> samFiles,
SAMFileReader.ValidationStringency strictness,
Double downsampleFraction,
Integer downsampleCoverage,
Boolean beSafe,
Boolean filterZeroMappingQualityReads ) {
List<SamRecordFilter> supplementalFilters ) {
this.readsFiles = samFiles;
this.validationStringency = strictness;
this.downsamplingFraction = downsampleFraction;
this.downsampleToCoverage = downsampleCoverage;
this.beSafe = beSafe;
this.filterZeroMappingQualityReads = filterZeroMappingQualityReads;
this.supplementalFilters = supplementalFilters;
}
}

45
java/src/org/broadinstitute/sting/gatk/WalkerManager.java
View File

@ -8,19 +8,14 @@ import java.util.HashMap;
import java.util.Map;
import java.util.Arrays;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.walkers.WalkerName;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.By;
import org.broadinstitute.sting.gatk.walkers.Allows;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.RMD;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
import org.broadinstitute.sting.utils.JVMUtils;
import org.broadinstitute.sting.utils.PathUtils;
import org.broadinstitute.sting.utils.StingException;
import org.apache.log4j.Logger;
import net.sf.picard.filter.SamRecordFilter;
/**
* Created by IntelliJ IDEA.
@ -185,6 +180,30 @@ public class WalkerManager {
return Arrays.asList(requiresDataSource.referenceMetaData());
}
/**
* Extracts filters that the walker has requested be run on the dataset.
* @param walker Walker to inspect for filtering requests.
* @return A non-empty list of filters to apply to the reads.
*/
public static List<SamRecordFilter> getReadFilters(Walker walker) {
Class<? extends SamRecordFilter>[] filterTypes = getReadFilterTypes(walker);
List<SamRecordFilter> filters = new ArrayList<SamRecordFilter>();
for( Class<? extends SamRecordFilter> filterType: filterTypes ) {
try {
filters.add(filterType.newInstance());
}
catch( InstantiationException ex ) {
throw new StingException("Unable to instantiate filter: " + filterType, ex);
}
catch( IllegalAccessException ex ) {
throw new StingException("Unable to access filter: " + filterType, ex);
}
}
return filters;
}
/**
* Load classes internal to the classpath from an arbitrary location.
*
@ -280,4 +299,16 @@ public class WalkerManager {
Allows allowsDataSource = walkerClass.getAnnotation(Allows.class);
return allowsDataSource;
}
/**
* Gets the list of filtering classes specified as walker annotations.
* @param walker The walker to inspect.
* @return An array of types extending from SamRecordFilter. Will never be null.
*/
private static Class<? extends SamRecordFilter>[] getReadFilterTypes(Walker walker) {
Class<? extends Walker> walkerClass = walker.getClass();
if( !walkerClass.isAnnotationPresent(ReadFilters.class) )
return new Class[0];
return walkerClass.getAnnotation(ReadFilters.class).value();
}
}

26
java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java
View File

@ -16,6 +16,7 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.sam.SAMReadViolationHistogram;
import java.io.File;
import java.util.List;
/*
* Copyright (c) 2009 The Broad Institute
@ -133,15 +134,15 @@ public class SAMDataSource implements SimpleDataSource {
iterator = applyDecoratingIterators(true,
iterator,
reads.getDownsamplingFraction(),
reads.getFilterZeroMappingQualityReads(),
reads.getSafetyChecking());
reads.getSafetyChecking(),
reads.getSupplementalFilters());
} else if (shard.getShardType() == Shard.ShardType.LOCUS || shard.getShardType() == Shard.ShardType.INTERVAL) {
iterator = seekLocus(shard.getGenomeLoc());
iterator = applyDecoratingIterators(false,
iterator,
reads.getDownsamplingFraction(),
reads.getFilterZeroMappingQualityReads(),
reads.getSafetyChecking());
reads.getSafetyChecking(),
reads.getSupplementalFilters());
} else {
throw new StingException("seek: Unknown shard type");
}
@ -362,15 +363,15 @@ public class SAMDataSource implements SimpleDataSource {
* @param enableVerification Verify the order of reads.
* @param wrappedIterator the raw data source.
* @param downsamplingFraction whether and how much to downsample the reads themselves (not at a locus).
* @param filterZeroMappingQualityReads whether to filter zero mapping quality reads.
* @param beSafeP Another trigger for the verifying iterator? TODO: look into this.
* @param supplementalFilters additional filters to apply to the reads.
* @return An iterator wrapped with filters reflecting the passed-in parameters. Will not be null.
*/
private StingSAMIterator applyDecoratingIterators(boolean enableVerification,
StingSAMIterator wrappedIterator,
Double downsamplingFraction,
Boolean filterZeroMappingQualityReads,
Boolean beSafeP) {
Boolean beSafeP,
List<SamRecordFilter> supplementalFilters) {
// NOTE: this (and other filtering) should be done before on-the-fly sorting
// as there is no reason to sort something that we will end of throwing away
if (downsamplingFraction != null)
@ -379,19 +380,12 @@ public class SAMDataSource implements SimpleDataSource {
if (beSafeP != null && beSafeP && enableVerification)
wrappedIterator = new VerifyingSamIterator(wrappedIterator);
if ( filterZeroMappingQualityReads != null && filterZeroMappingQualityReads )
for( SamRecordFilter supplementalFilter: supplementalFilters )
wrappedIterator = StingSAMIteratorAdapter.adapt(wrappedIterator.getSourceInfo(),
new FilteringIterator(wrappedIterator, new ZeroMappingQualityReadFilterFunc()));
new FilteringIterator(wrappedIterator,supplementalFilter));
return wrappedIterator;
}
private static class ZeroMappingQualityReadFilterFunc implements SamRecordFilter {
public boolean filterOut(SAMRecord rec) {
return (rec.getMappingQuality() == 0);
}
}
}

42
java/src/org/broadinstitute/sting/gatk/filters/ZeroMappingQualityReadFilter.java 100644
View File

@ -0,0 +1,42 @@
/*
* Copyright (c) 2009 The Broad Institute
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord;
/**
* Filter out zero mapping quality reads.
*
* @author hanna
* @version 0.1
*/
public class ZeroMappingQualityReadFilter implements SamRecordFilter {
public boolean filterOut(SAMRecord rec) {
return (rec.getMappingQuality() == 0);
}
}

34
java/src/org/broadinstitute/sting/gatk/filters/package.html 100644
View File

@ -0,0 +1,34 @@
<!--
~ Copyright (c) 2009 The Broad Institute
~ Permission is hereby granted, free of charge, to any person
~ obtaining a copy of this software and associated documentation
~ files (the "Software"), to deal in the Software without
~ restriction, including without limitation the rights to use,
~ copy, modify, merge, publish, distribute, sublicense, and/or sell
~ copies of the Software, and to permit persons to whom the
~ Software is furnished to do so, subject to the following
~ conditions:
~
~ The above copyright notice and this permission notice shall be
~ included in all copies or substantial portions of the Software.
~
~ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
~ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
~ OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
~ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
~ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
~ WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
~ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
~ OTHER DEALINGS IN THE SOFTWARE.
-->
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
"http://www.w3.org/TR/html4/loose.dtd">
<html>
<head>
<title></title>
</head>
<body>
Provides a commonly used set of filters for determining which data should and should not be applied.
</body>
</html>

6
java/src/org/broadinstitute/sting/gatk/walkers/PrintLocusContextWalker.java
View File

@ -1,12 +1,10 @@
package org.broadinstitute.sting.gatk.walkers;
import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import java.util.List;
import java.util.Arrays;
import java.util.ArrayList;
import net.sf.samtools.SAMRecord;
@ -17,8 +15,8 @@ import net.sf.samtools.SAMRecord;
* Time: 11:23:14 AM
* To change this template use File | Settings | File Templates.
*/
public class PrintLocusContextWalker extends LocusWindowWalker<LocusContext, Integer> implements TreeReducible<Integer> {
public LocusContext map(RefMetaDataTracker tracker, String ref, LocusContext context) {
public class PrintLocusContextWalker extends LocusWalker<LocusContext, Integer> implements TreeReducible<Integer> {
public LocusContext map(RefMetaDataTracker tracker, char ref, LocusContext context) {
out.printf( "In map: ref = %s, loc = %s, reads = %s%n", ref,
context.getLocation(),
Arrays.deepToString( getReadNames(context.getReads()) ) );

7
java/src/org/broadinstitute/sting/gatk/walkers/RMD.java
View File

@ -1,6 +1,8 @@
package org.broadinstitute.sting.gatk.walkers;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import java.lang.annotation.*;
/**
* User: hanna
* Date: May 19, 2009
@ -17,7 +19,10 @@ import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
/**
* A data type representing reference-ordered data.
*/
@Documented
@Inherited
@Retention(RetentionPolicy.RUNTIME)
@Target(ElementType.TYPE)
public @interface RMD {
String name();
Class<? extends ReferenceOrderedDatum> type();

43
java/src/org/broadinstitute/sting/gatk/walkers/ReadFilters.java 100644
View File

@ -0,0 +1,43 @@
/*
* Copyright (c) 2009 The Broad Institute
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.walkers;
import net.sf.picard.filter.SamRecordFilter;
import java.lang.annotation.*;
/**
* An annotation to describe what kind of data will be filtered out.
*
* @author hanna
* @version 0.1
*/
@Documented
@Inherited
@Retention(RetentionPolicy.RUNTIME)
@Target(ElementType.TYPE)
public @interface ReadFilters {
public Class<? extends SamRecordFilter>[] value() default {};
}

3
java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java
View File

@ -3,8 +3,10 @@ package org.broadinstitute.sting.playground.gatk.walkers;
import net.sf.samtools.SAMReadGroupRecord;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.ReadFilters;
import org.broadinstitute.sting.playground.utils.AlleleFrequencyEstimate;
import org.broadinstitute.sting.playground.utils.AlleleMetrics;
import org.broadinstitute.sting.playground.utils.GenotypeLikelihoods;
@ -20,6 +22,7 @@ import java.io.FileNotFoundException;
import java.io.PrintStream;
import java.util.List;
@ReadFilters(ZeroMappingQualityReadFilter.class)
public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate, String> {
// Control output settings
@Argument(fullName="variants_out", shortName="varout", doc="File to which variants should be written", required=true) public File VARIANTS_FILE;

8
java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java
View File

@ -151,6 +151,11 @@ public abstract class CommandLineProgram {
return null;
}
static {
// setup a basic log configuration
BasicConfigurator.configure();
}
/**
* This function is called to start processing the command line, and kick
* off the execute message of the program.
@ -161,9 +166,6 @@ public abstract class CommandLineProgram {
public static void start(CommandLineProgram clp, String[] args) {
try {
// setup a basic log configuration
BasicConfigurator.configure();
// setup our log layout
PatternLayout layout = new PatternLayout();